Experiments from the book can be selected through the
Experiments menu. The number of the experiment in the book is given in
parentheses. To create your own one or two cell system click on Create Your
Own. Graphs of the voltage or calcium dependency of the asymptotic gate
values and time constants can be selected through the Plot Currents menu.
The Session menu has options to save and restore parameters and graphs.
The Other menu a.o. allows advanced users to pop up the NEURON main panel
if desired. The Init & Run button initializes and
starts a simulation, the Stop after button determines the
duration (in ms).
Parameters in the demo
The user has control over a wide range of parameters through the parameter panel. To discriminate between properties of different ionic channels, NEURON suffixes all parameters and variables with _ and the current name. For example, in the Experiments section of MyFirstNEURON you will encounter current names such as leak, HH, iA, iAHP, iC, iL, iM, iT. On the other hand, properties of synaptic currents are accessed as object variables, i.e. the parameters and variables are prefixed, with for example ampasyn, nmdasyn, gabaA, gabaB. When modifying values in the paramater panel, a red check will appear, the old value can be restored by clicking on the red check.
Maximum permeabilities are denoted as pionnamebar (or pionname for the leak currents) and maximum conductances as gionnamebar. Note that the units for the conductances, permeabilities, and ionic currents are measured per unit membrane area, whereas in the book these units are taken per total membrane area (29,000 um2 ).
The ionic concentrations that can be manipulated are the internal and external concentrations of sodium (nai/nao), potassium (ki/ko), calcium (cai/cao), chloride (cli/clo), and the external concentration of magnesium (mgo).
The synaptic properties that can be modified in the Experiments section include the onset and maximum conductance (in nS) of the postsynaptic current, and a weight value that scales the maximum conductance for the four individual synaptic currents.
Base current is a constant current injection during the entire experiment.
Negative base currents will hyperpolarize the cell. Another current clamp
electrode can be specified to inject for a certain duration
a constant current after an initial delay. A voltage
clamp pair of electrodes can be specified to clamp the soma at three different
voltages amp0, amp1,
amp2 for durations of dur0, dur1, dur2, respectively. The Run Series button will run a voltage clamp series from the
minimal to the maximal voltage value as displayed on the axis of the voltage
plot. To prevent the plots of the individual steps to be erased, select the
keep lines option with the right mouse button in the appropriate graphs.
The size of the axes can be changed with the set view option under the view... menu that pops up by clicking the right mouse button in any graph. To change the color and/or thickness of any line choose colorbrush, select your favorite color, and click with the cursor on the lines or labels you want to change. To read off the exact values of a plot select crosshair and click closely on your plotted line. To plot additional variables take the plot what? option and a selector will pop up. If you want to plot the state of an ionic channel, a concentration or current, browse down and double click on soma. Now, a second list will appear with all the available variables to plot. For a synaptic variable, select one of the synapse objects in the first list.
Speed & accuracy of simulations and plots
Advanced users may want to change the accuracy/speed of the simulation. To do
this, change the integration time step (default value 0.05 ms) through the interpretor by typing dt =
desired value. Increasing the integration
time step will speed up your simulation, however, significant errors may be
introduced in your calculations. Another way to increase the speed of your
simulation is to decrease the time NEURON spends on plotting curves. This can be
done by reducing the number of points plotted per time unit in the graphs
(default 10 points/ms). To do this, go to the interpretor
and type steps_per_ms = desired
Asymptotic gate values and time constants
The asymptotic gate values reflect what fraction of
channels will be open if the cell had been clamped at a certain voltage value
for a sufficiently long time. For example, in the accompanying upper plot we can
see in red the proportion of open activation gates of the sodium channel
responsible for spike generation, given for voltage clamp values between -100
and 50 mV. Identically, the blue line displays the fraction of open inactivation
gates. In the lower plot, we can see the corresponding time constants for
opening and closing of the gates. The axes can be rescaled the same way as
described above. For some currents, the fraction of open gates depends on the
internal calcium concentration, and a calcium plot can be selected under
Abscissa. In this case, the Init V button displays
the voltage at which the soma is clamped and
[Ca2+]i is the varying variable (default from 0-1
mM). By changing the temperature of the experiment time constants may
Saving and retrieving parameter values and graphs
To save your parameters and graphs go to the Print & File Window manager that automatically pops up when you start MyFirstNEURON. First, select the icon representing the parameter panel in the left virtual screen by clicking on it with the right mouse button. Then, select the icon representing the graph panel. Unfortunately, this specific order is crucial for retrieval of your graphs. To unselect a selected icon, go to the right virtual screen and press the right mouse button on the icon. Press the PFWM Session button, choose Save selected, and enter a filename. To restore your session use the Retrieve option under the Session menu on the demo main panel and type the filename.
Create your own system
In the Create Your Own section the user chooses from a larger set of mechanisms which to insert into the membrane by pressing the Insert/Remove Mechanisms button. After the membrane has been configured the Create Parameter Panel button will pop up a panel with the parameters that are relevant to the inserted mechanisms. If you decide to insert new or uninsert inserted mechanisms the parameter panel will be adjusted by pressing the button again.
Parameters that were not encountered in the Experiments section include a.o. the diameter diam (um) and capacitance cm (uF/cm2 ) of the cell, the equilibrium potentials ecan and eh of the ICAN and H-current respectively, the depth depth_cadyn (um) of the thin calcium diffusion shell under the membrane, the time constant taur_cadyn (ms) and equilibrium concentration cainf_cadyn (mM) of intracellular calcium diffusion, the time constant kt_cadyn and equilibrium calcium value kd_cadyn of the calcium ATPase pump. If the calcium diffusion & pump mechanism is inserted the initial internal calcium concentration will be set to the equilibrium value of the pump, and use cao0_ca_ion to set the external calcium concentration from the command line (default 2 mM).
The synapses in the Create Your Own section are more advanced than the alpha synapses in the Experiments section. Every time a spike arrives, a rectangular transmitter pulse is generated. Transmitter binding is modeled as a first order kinetic system (see for brief explanation e.g. ampa2.mod). Also, the frequency of release of the synapses can be specified.
Graphs can be created with Create Graph button on the main control as described above. When plotting variables the name of the cell in question should dot prefix the variable. The one cell system is called soma, the two cells in the interconnected system are called cell1 and cell2.
To save and restore your cell definition, parameter values and graphs choose the Session option on the main panel. It is important to always restore your sessions in the appropriate environment (Experiments, My Own Cell, or My Two Cells).
Global values in the mod files can be modified by popping up the NEURON main panel under the Other menu, followed by the option sequence Distributed Mechanisms, Viewers, Mechanisms (Globals). Global modifications are not automatically saved, if desired the user should save the modified global parameter panels with the other parameter panels and graphs as described above.
Advanced users may want to modify the equations that describe channels, synapses, and calcium dynamics by editing the mod files in question, or own mod files can be added if desired. Click here for information on the model description language. After modifying or adding mod files, special should always be recompiled with the nrnivmodl command.